Not sure if it matters, but before I make some mistake that will cause a lot of work to correct afterwards: Why are some sublayers not colored like the partent-layer (see screenshot)? Are they somehow linked to other layers?
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most probably because they used to be part of a differently colored sublayer – joojaa Oct 20 '14 at 4:58
They aren't linked, colors are only used to visually be able to differentiate objects from the different layers. When you select an object, its outline will have the same color as the layer color.
I guess that Adobe chose to not make the sub layers the same color because they guessed(?) that users would like it that way...
